Reproducible data analysis with R and Quarto

Magnus Johansson, PhD

RISE Research Institutes of Sweden

2023-06-12

Ambitions with this course

  • It is not a statistics course
  • We’ll cover the basics of using R, Rstudio and Quarto
  • More advanced things will be addressed at later sessions
    • requests are welcome
  • I like pragmatic learning, so we’ll use practical examples for most things

Expectations and hopes

I hope that you will be fairly comfortable with:

  • importing a dataset & doing basic analysis
  • documenting your analysis alongside your code
    • creating an output document
  • getting something out of the many online articles using R for analysis
  • searching the internet for help

Words of wisdom

https://datavizs23.classes.andrewheiss.com/slides/15-slides.html#62

Overview for today

  • the basics of using Rstudio
  • the basics of setting up and using Quarto (in Rstudio)
  • a tiny bit of really basic R functions
  • importing data (and naming variables)
  • data wrangling
  • descriptive analysis & visualization
  • modeling & visualization

Keyboard shortcuts

You will benefit greatly from doing things cleverly and establishing good habits from the start

  • avoid unnecessary typing and using the mouse/trackpad

I have prepared a handout containing the most frequently used shortcuts

  • We’ll walk through them later on, and you have the handout as a reference

Fundamentals

  • never touch your datafile manually!!!
    • everything you do with your data needs to be documented
  • Don’t erase code/things you try (only erase faulty code)
    • you need to be able to retrace your steps
    • makes it easier to involve others
    • You can copy&paste selected part of your code later if you need to clean up for publication/sharing

Good things

  • Traceability
    • Transparency in decision making during analysis
  • Reproducibility
  • We use freely available tools
  • Documentation in the same file as analysis code

Levels of reproducibility

Meme credit: https://bookdown.org/pdr_higgins/rmrwr/introduction-to-reproducibility.html#cleaning-and-analyzing-your-data

Rstudio layout

  • 4 quadrants with tabs in each
    • code, console, environment & output/help
  • projects!
  • outline & line numbers
  • moving a code tab to a separate window
  • code editor is helpful and sometimes confusing

Quarto basics

  • YAML
  • code chunks & chunk output
  • source view and “visual”
  • headings and structure
  • labelling with tbl- and fig-
  • (panel-tabset)

Basics about R

  • based on functions() and objects
    • functions do things with data
    • objects store data and output from functions
  • let’s first skim basic definitions, then go to practical examples
  • decimal symbol is always .! Commas are used to separate things.

Functions

  • a function always has () tied to it
  • various settings within a function are divided by ,
  • we can pipe/forward an object or function output to another function
    • there are two pipes (we’ll only use the first one)
    • %>% - the magrittr pipe (shift+ctrl+m)
    • |> - the base pipe

Function syntax

  • comma separates input within the parantheses
    • hist(data, xlab = "Distribution of variable")
  • use the Help tab in lower right quadrant (or ?function in console)

Objects

  • objects can have many different classes/formats
  • we will mostly work with dataframes
    • similar to what you see in a spreadsheet file (Excel)
    • they consist of vectors (rows and columns)
    • a vector is a string of values
  • each object or column in a dataframe can have a different class
    • we will primarily work with
    • character (chr)
    • factor (fct)
    • numerical (num, int, or dbl)

Simple object examples

Single values

number <- 1
number <- "1"

Multiple values (a vector)

number <- c(1,2)
number <- c("one","two")

Dataframes

df <- read_excel("path/to/excelfile.xls", sheet = 1)
  • A dataframe is a collection of rows (vectors) and columns (also vectors).

Keyboard shortcuts

  • TAB-completion TAB-tangenten har många funktioner, dels kan den fylla i objekt- eller funktionsnamn när du skriver kod, men även i sökvägar när du ska läsa en fil.
  • CTRL+enter Kör kodraden du har markören på (och hoppar ner till nästa). Om du har ett block med flera rader av tidy-kod som hålls samman med pipe-symbolen %\>% som radbrytning, eller ggplot-kod (som hålls samman med +) så spelar det ingen roll var bland raderna markören är, hela blocket körs ändå
  • CTRL+SHIFT+enter Kör en hel code chunk i Quarto. Spelar ingen roll var i chunken du har markören.
  • CTRL+SHIFT+m Skapar en pipe-symbol
  • CTRL+ALT(option)+i Skapar en ny code chunk i Quarto
  • CTRL/CMD+SHIFT+c Kommentera bort/in alla rader som är markerade